Clustal 2 comes in two flavors: the command-line version Clustal W and the graphical version Clustal X. Precompiled executables for Linux, Mac OS X and Windows (incl.XP and Vista) of the most recent version (currently 2.1) along with the source code are available for download here. You can also browse for older versions (Clustal W 1.81, Clustal V etc). The current version of Clustal 2 is also mirrored on the EBI ftp site .
Clustal X Download For Mac
Download Zip: https://cuphowviefu.blogspot.com/?download=2vGg7d
Please have a look at Clustal X's builtin help menu or if you are using Clustal W use clustalw[2] -help or /help (depending on your platform and version of Clustal). Online versions (which might be out of date) can be found here: Clustal W and Clustal X. There are a couple of references on how to use Clustal W/X on the net. A very nice tutorial which also covers advanced features like using secondary structures for profile alignment is "Using Clustal X for multiple sequence" by Jarno Tuimala (local mirror).
Installation instructions are available in the INSTALL file, once the archive is extracted. This release is intended for use with UNIX systems. Installation on Macs is also possible. Windows users should download the binary release below.
Windows users should extract the zip file and read the enclosed INSTALL.txt. UNIX and Mac users should rename the downloaded file to clustalo and place in the location of their choice. This file may need to be made executable e.g.: chmod u+x clustalo
CodonCode Aligner - Newer software for sequence alignment and sequence assembly on Windows and Mac OS X. Free trial downloads. Published prices, significantly less expensive than other popular packages. One useful and unique feature is the ability to align assembled contigs with Clustal or MUSCLE to create "contigs of contigs".
Note for MS Windows users:The downloaded file (seaview5.exe) is a self-extracting archive: open it, and it will create a folder called seaview5on your computer.The window that appears when you open seaview5.exe allows you to choose where to place the seaview5 folder.This folder contains the seaview program, an example data file, a .html file, and 5 other programs(muscle, clustalo, phyml, Gblocks, treerecs) that seaview drives. This folder contains also seaview32bit.exe, a 32-bit version of theseaview program. If you run a 32-bit version of MS Windows (typically Windows XP), you can discard seaview.exeand use seaview32bit.exe.Note for Linux/Unix users:The downloaded archives contain the seaview executable itself, an example data file, a .html file, and 5 other programs(muscle, clustalo, phyml, Gblocks, treerecs) that seaview drives. These 5 programs and the .html file can either be left in thesame directory as seaview, or be put in any directory of your PATH.
Clustalx uses the same algorithms as clustalw. However, it has a much nicer interface, it displays information on the level of similarity, and it uses color in the alignment. Especially for amino acids the use of color greatly enhances the ability to recognize conservative replacements. Clustalx2.1 is available for different platforms at the ebi's ftp site (follow your platform, clustalx is stored in the clustalw folders)
> name of sequence or any other information goes in the first line. This line starts with ">". The line can be longer than 80 characters. The first line ends with the first paragraph sign.p The second line contains the sequence itself; numbers and other non standard characters are ignored. Be careful if you download sequences. Often the transfer programs introduce paragraph signs every 100 characters, and the end of a command line frequently ends up as the beginning of the sequence. All sequences to be read should be in a single file.
Clustal also is useful to reformat and edit alignments, it is very forgiving in reading formats, e.g., you can open the clustal format (*.aln) in a text editor and delete columns and reload the file into clustalw, and output it in the other formats available.
It is important to realize that the second step is the most important. The relationships found here will create a serious bias in the final alignment. The better your guide tree, the better your final alignment. You can load a guide tree into clustal. This tree will then be used instead of the neighbor joining tree calculated by clustalw as a default. (The guide tree needs to be in normal parenthesis notation WITH branch lengths).
MUSCLE is the current alignment program of choice. It is thought to give better alignments compared to clustal, it is faster and works with larger datasets. The program is available through a webserver at the ebi, and as a commandline program to download here.
One useful sequence editor is seaview. It runs on PC and most unix flavors (including Macs). The latest version (4.5) includes phylogenetic reconstruction using phyml and parsimony, multiple sequence alignment using clustalw and muscle, and filtering of poorly aligned regions using GBlocks.
If you have a list of known accession numbers that you wish to download, you can enter these in the Search box separated by a comma. For consecutive accessions, enter the first and last numbers separated by a colon, and append [accn] to this. E.g. Entering "AB000001:AB000009[accn]" will download all accessions between AB000001 and AB000009.
The results will appear in the Document table as they are found. The Search button changes to a Stop button while the search is running, and this can be clicked at any time to terminate the search. As the results are downloaded, you will see a small padlock icon in the status bar above the Document Table, which indicates that these items cannot be modified in any way. You must drag the file into a folder in your local database if you wish to retain the file and/or modify it. If you don't drag the documents from a database search into your local folders the results will be lost when Geneious is closed. For more information on how to move files between folders in your database, see Moving files around.
Note: When searching the Genome, Gene or PopSet databases, the documents returned are only summaries. To download the whole genome, select the summary(s) of the genome(s) you would like to download and the click the Download button inside the document view or just above it. Alternatively you can choose Download Documents in the File menu and in the popup menu when document summary is right-clicked (Ctrl+click on Mac OS X). The size of these files is not displayed in the Documents Table. Be aware that whole genomes can be very large and can take a long time to download. You can cancel the download of document summaries by selecting Cancel Downloads from any of the locations mentioned above.
NCBI was established in 1988 as a public resource for information on molecular biology. Geneious allows you to directly download information from eight important NCBI databases and perform NCBI BLAST searches.
Note: If the full text of the article is available for download in PDF format, it can also be stored in Geneious by saving it to your hard drive and then importing it. This will allow full-text searches to be performed on the article. To view a .pdf document either double click on the document in the Documents Table or click on the View Document button. This opens the document in an external PDF viewer such as Adobe Acrobat Reader or Preview (Mac OS X). On Linux, you can set an environmental variable named "PDFViewer" to the name of your external PDF viewer. The default viewers on Linux are kpdf and evince.
Clustal Omega binaries are available here: SEDA was developed and tested using the version 1.2.4, which is the version included in the official Docker image ( -clustalomega/dockerfile).
The original Splign and Compart binaries are available here: =downloads. Nevertheless, it is recommended to use the following binaries: -group.org/software/SEDA/dev_resources/splign-compart.tar.gz. This version is the one included in the official Docker image ( -splign-compart).
Often for repeat sequences, you can use the self-chain track to find the other matches, but only if the other matches are long and specific enough. You can check whether any sequence is present at a particular location by using the "Short match" track if your sequence is less than 30 bp.You can work around this minimum length limitation by adding more flanking sequence to your queryto make the query unique enough. If this is not possible, the only alternative is to download the executables of BLAT and the .2bit file of a genome to your own machine and use BLAT on the command line. See Downloading BLAT source and documentation for more information. When using the command line version of BLAT, you can set the repMatch option to a large value to try to improve finding matches in repetitive regions and do notuse one of the default 11.ooc repeat masking files.
Alternatively, you can try filtering your Blat PSL output using either thepslReps or pslCDnaFilter program available in the Genome Browser source code. For information on obtaining the source code, see our FAQ on source code licensing and downloads.
A note on filtering output: increasing the -minScore parameter value beyond one-half of the query size has no further effect. Therefore, use either the pslReps or pslCDnaFilter program available in the Genome Browser source code to filter for the size, score, coverage, or quality desired. For information on obtaining the source code, see our FAQ on source code licensing and downloads.
Often times using the gfServer/gfClient provides a better approximation or even replicate ofthe web-based Blat results, which otherwise cannot be found using standalone Blat. This approachmimics the Blat server used by the Genome Browser web-based Blat. The following example will showhow to set up an hg19 gfServer, then make a query. First, download the appropriate utility forthe operating system and give it executable permissions: 2ff7e9595c
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